Sounds like that probably is contributing to the ear problem. But don't beat yourself up about it...mothering is an adventure, and at least half of the time we all have no clue what we're doing, and that includes those of us that have a handful of kids! lol... It's a, "learn-as-you-go," process. :)
Find a milk-free acidopholous/probiotics source to build up his intestinal flora after this round of Antibiotics , and lay off all the milk (even in the cheddar bunnies, etc--you'll become an avid label reader), and I bet he'll be just fine (and you'll probably see a notable improvement in his skin, as well).